[2023-03-17 08:11:32,981] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,981] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference
[2023-03-17 08:11:34,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:34,670] [INFO] Task started: Prodigal
[2023-03-17 08:11:34,670] [INFO] Running command: cat /var/lib/cwl/stg5b39e30b-1bd1-4ebe-8a5c-6d8caa9faf58/OceanDNA-b6645.fa | prodigal -d OceanDNA-b6645/cds.fna -a OceanDNA-b6645/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:54,563] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:54,564] [INFO] Task started: HMMsearch
[2023-03-17 08:11:54,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b6645/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/reference_markers.hmm OceanDNA-b6645/protein.faa > /dev/null
[2023-03-17 08:11:54,766] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:54,767] [INFO] Found 6/6 markers.
[2023-03-17 08:11:54,785] [INFO] Query marker FASTA was written to OceanDNA-b6645/markers.fasta
[2023-03-17 08:11:54,786] [INFO] Task started: Blastn
[2023-03-17 08:11:54,787] [INFO] Running command: blastn -query OceanDNA-b6645/markers.fasta -db /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/reference_markers.fasta -out OceanDNA-b6645/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:55,427] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:55,428] [INFO] Selected 14 target genomes.
[2023-03-17 08:11:55,428] [INFO] Target genome list was writen to OceanDNA-b6645/target_genomes.txt
[2023-03-17 08:11:55,437] [INFO] Task started: fastANI
[2023-03-17 08:11:55,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b39e30b-1bd1-4ebe-8a5c-6d8caa9faf58/OceanDNA-b6645.fa --refList OceanDNA-b6645/target_genomes.txt --output OceanDNA-b6645/fastani_result.tsv --threads 1
[2023-03-17 08:12:04,393] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:04,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:04,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:04,403] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:04,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:04,403] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	84.4366	774	1046	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	83.2442	767	1046	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	80.9444	657	1046	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	80.7423	568	1046	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.5483	378	1046	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.1693	389	1046	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1547	385	1046	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	78.1346	336	1046	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.0359	371	1046	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.8795	331	1046	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.8167	261	1046	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.652	267	1046	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.3895	231	1046	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.176	258	1046	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:04,403] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6645/tc_result.tsv
[2023-03-17 08:12:04,403] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:04,403] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:04,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/checkm_data
[2023-03-17 08:12:04,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:04,408] [INFO] Task started: CheckM
[2023-03-17 08:12:04,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6645/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6645/checkm_input OceanDNA-b6645/checkm_result
[2023-03-17 08:12:54,985] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:54,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:54,988] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:54,988] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:54,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6645/markers.fasta)
[2023-03-17 08:12:54,989] [INFO] Task started: Blastn
[2023-03-17 08:12:54,989] [INFO] Running command: blastn -query OceanDNA-b6645/markers.fasta -db /var/lib/cwl/stg03f577d7-5959-464f-b34e-a261a2017ebe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6645/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:55,941] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:55,941] [INFO] Selected 8 target genomes.
[2023-03-17 08:12:55,942] [INFO] Target genome list was writen to OceanDNA-b6645/target_genomes_gtdb.txt
[2023-03-17 08:12:55,949] [INFO] Task started: fastANI
[2023-03-17 08:12:55,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b39e30b-1bd1-4ebe-8a5c-6d8caa9faf58/OceanDNA-b6645.fa --refList OceanDNA-b6645/target_genomes_gtdb.txt --output OceanDNA-b6645/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:01,714] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:01,719] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:13:01,720] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002414705.1	s__Algorimicrobium sp002414705	99.8128	939	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008086165.1	s__Algorimicrobium algoritergicola	84.4366	774	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900115185.1	s__Algorimicrobium echini	83.2329	768	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	80.9381	658	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224335.1	s__Algorimicrobium argentinense	80.7463	568	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	78.141	357	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	78.1154	297	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.8422	281	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:01,720] [INFO] GTDB search result was written to OceanDNA-b6645/result_gtdb.tsv
[2023-03-17 08:13:01,720] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:01,721] [INFO] DFAST_QC result json was written to OceanDNA-b6645/dqc_result.json
[2023-03-17 08:13:01,721] [INFO] DFAST_QC completed!
[2023-03-17 08:13:01,721] [INFO] Total running time: 0h1m29s